Fix imports

cg/meta/workflow/microsalt/__init__.py

@@ -0,0 +1,2 @@
+from .microsalt import MicrosaltAnalysisAPI
+from .quality_checker import QualityChecker

cg/meta/workflow/microsalt/quality_checker.py

@@ -5,13 +5,14 @@
 
 from cg.constants.constants import MicrosaltAppTags, MicrosaltQC
 from cg.models.orders.sample_base import ControlEnum
+from cg.store.api.core import Store
 from cg.store.models import Sample
 
 LOG = logging.getLogger(__name__)
 
 
 class QualityChecker:
-    def __init__(self, status_db):
+    def __init__(self, status_db: Store):
         self.status_db = status_db
 
     def microsalt_qc(self, case_id: str, run_dir_path: Path, lims_project: str) -> bool:
@@ -106,7 +107,6 @@ def check_external_negative_control_sample(self, sample: Sample) -> bool:
             * MicrosaltQC.NEGATIVE_CONTROL_READS_THRESHOLD
         )
 
-
     def is_qc_required(self, case_run_dir: Path | None, case_id: str) -> bool:
         """Checks if a qc is required for a microbial case."""
         if case_run_dir is None:

tests/meta/workflow/test_microsalt.py

@@ -6,7 +6,7 @@
 from cg.apps.tb.api import TrailblazerAPI
 
 from cg.constants.constants import CaseActions, Pipeline
-from cg.meta.workflow.microsalt import MicrosaltAnalysisAPI
+from cg.meta.workflow.microsalt import MicrosaltAnalysisAPI, QualityChecker
 from cg.models.cg_config import CGConfig
 from cg.models.orders.sample_base import ControlEnum
 from cg.store import Store
@@ -33,10 +33,10 @@ def test_qc_check_fail(
     for index in range(4):
         microsalt_case.samples[index].reads = 1000
 
-    mocker.patch.object(MicrosaltAnalysisAPI, "create_qc_done_file")
+    mocker.patch.object(QualityChecker, "create_qc_done_file")
 
     # WHEN performing QC check
-    qc_pass: bool = microsalt_api.microsalt_qc(
+    qc_pass: bool = microsalt_api.quality_checker.microsalt_qc(
         case_id=microsalt_case_qc_fail,
         run_dir_path=microsalt_qc_fail_run_dir_path,
         lims_project=microsalt_qc_fail_lims_project,
@@ -65,10 +65,10 @@ def test_qc_check_pass(
     microsalt_case.samples[1].control = ControlEnum.negative
     microsalt_case.samples[1].reads = 1100000
 
-    mocker.patch.object(MicrosaltAnalysisAPI, "create_qc_done_file")
+    mocker.patch.object(QualityChecker, "create_qc_done_file")
 
     # WHEN performing QC check
-    qc_pass: bool = microsalt_api.microsalt_qc(
+    qc_pass: bool = microsalt_api.quality_checker.microsalt_qc(
         case_id=microsalt_case_qc_pass,
         run_dir_path=microsalt_qc_pass_run_dir_path,
         lims_project=microsalt_qc_pass_lims_project,
@@ -97,10 +97,10 @@ def test_qc_check_negative_control_fail(
     microsalt_case: Case = store.get_case_by_internal_id(internal_id=microsalt_case_qc_fail)
     microsalt_case.samples[0].control = ControlEnum.negative
 
-    mocker.patch.object(MicrosaltAnalysisAPI, "create_qc_done_file")
+    mocker.patch.object(QualityChecker, "create_qc_done_file")
 
     # WHEN performing QC check
-    qc_pass: bool = microsalt_api.microsalt_qc(
+    qc_pass: bool = microsalt_api.quality_checker.microsalt_qc(
         case_id=microsalt_case_qc_fail,
         run_dir_path=microsalt_qc_fail_run_dir_path,
         lims_project=microsalt_qc_fail_lims_project,
@@ -175,7 +175,7 @@ def test_get_cases_to_store_pass(
     caplog.set_level(logging.INFO)
     store = qc_microsalt_context.status_db
     microsalt_api: MicrosaltAnalysisAPI = qc_microsalt_context.meta_apis["analysis_api"]
-    mocker.patch.object(MicrosaltAnalysisAPI, "create_qc_done_file")
+    mocker.patch.object(QualityChecker, "create_qc_done_file")
     mocker.patch.object(TrailblazerAPI, "set_analysis_status")
     mocker.patch.object(TrailblazerAPI, "add_comment")
 
@@ -217,7 +217,7 @@ def test_get_cases_to_store_fail(
     caplog.set_level(logging.INFO)
     store = qc_microsalt_context.status_db
     microsalt_api: MicrosaltAnalysisAPI = qc_microsalt_context.meta_apis["analysis_api"]
-    mocker.patch.object(MicrosaltAnalysisAPI, "create_qc_done_file")
+    mocker.patch.object(QualityChecker, "create_qc_done_file")
     mocker.patch.object(TrailblazerAPI, "set_analysis_status")
     mocker.patch.object(TrailblazerAPI, "add_comment")